Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,638
datasets available to search
ShareScore release 0.9.0
Dataset results
1,638 results for “Mm.”
Supplementary material 1 from: Stampar SN, Gamero-Mora E, Maronna MM, Fritscher JM, Oliveira BSP, Sampaio CLS, Morandini AC (2020) The puzzling occurrence of the upside-down jellyfish Cassiopea (Cnidaria: Scyphozoa) along the Brazilian coast: a result of several invasion events? Zoologia 37: 1-10. https://doi.org/10.3897/zoologia.37.e50834
Figure S1. Map showing the collection localities of Cassiopea sequences used in the phylogenetic analysis. The green square refers to the site of collection of the population of C. andromeda from Alagoas, Brazil. Each color indicates a species. Cassiopea sp. 5 does not appear because of its unknown locality.
← Fig. 16. Liscocephala gen.n. and Triunfus gen.n. ♀: L. fumosa: A, C: female terminalia. T. carvalhoi: B, D: female terminalia; E, F: female receptaculum seminis and ausenwand. T. incarnatus: G: female receptaculum seminis and ausenwand. Scale bars = 0.5 mm. in Systematics of the Mecocephala group (Hemiptera: Heteroptera: Pentatomidae) based on a phylogenetic perspective: Inclusion of Hypanthracos, description of three new genera, and redescription of Ogmocoris
← Fig. 16. Liscocephala gen.n. and Triunfus gen.n. ♀: L. fumosa: A, C: female terminalia. T. carvalhoi: B, D: female terminalia; E, F: female receptaculum seminis and ausenwand. T. incarnatus: G: female receptaculum seminis and ausenwand. Scale bars = 0.5 mm.
→ Fig. 5. Hypanthracos meridionalis Grazia & Campos, 1996: A–F: male terminalia: A – D: dorsal; B – E: posterior: C – F: ventral; G – I: male genitalia: G: dorsal; H: lateral; I: ventral; J: female terminalia; K: female receptaculum seminis and ausenwand. Scale bars: A – F = 1.0 mm; G – I: 0.01 mm; J – K = 0.5 mm. in Systematics of the Mecocephala group (Hemiptera: Heteroptera: Pentatomidae) based on a phylogenetic perspective: Inclusion of Hypanthracos, description of three new genera, and redescription of Ogmocoris
→ Fig. 5. Hypanthracos meridionalis Grazia & Campos, 1996: A–F: male terminalia: A – D: dorsal; B – E: posterior: C – F: ventral; G – I: male genitalia: G: dorsal; H: lateral; I: ventral; J: female terminalia; K: female receptaculum seminis and ausenwand. Scale bars: A – F = 1.0 mm; G – I: 0.01 mm; J – K = 0.5 mm.
POPC @ 310K, 450 mM of CaCl_2. Charmm36 with ECC-scaled ions
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. <br> The goal was to study the effect of salt on the order <br> parameters of the lipid head group and the glycerol <br> backbone for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the recent ion parameters <br> by Kohagen et al. [2] for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained from<br> CHARMM-GUI [3] at http://www.charmm-gui.org</p> <p>The ion parameters are available at<br> https://bitbucket.org/hseara/ions/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. These data<br> were collected once the adsorption and desorption of <br> CaCl_2 to the surface has reached equilibrium, namely<br> after 700 ns of simulation. Additionally, the initial <br> structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.0–> (.tpr) and the energy output file <br> (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field <br> for Lipids: Validation on Six Lipid Types<br> Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, <br> Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, <br> Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor<br> The Journal of Physical Chemistry B 2010 114 (23), 7830-7843<br> DOI: 10.1021/jp101759q</p> <p>[2] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions<br> Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth<br> The Journal of Physical Chemistry B 2014 118 (28), 7902-7909<br> DOI: 10.1021/jp5005693</p> <p>[3] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, <br> and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field<br> Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, <br> Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, <br> Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, <br> Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im<br> Journal of Chemical Theory and Computation 2016 12 (1), 405-413<br> DOI: 10.1021/acs.jctc.5b00935</p>
POPC @ 310K, 450 mM of CaCl_2. Slipids with ECC-scaled ions
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. <br> The goal was to study the effect of salt on the order <br> parameters of the lipid head group and the glycerol <br> backbone for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The Slipids <br> model [1–3] is employed for lipids, tip3p model for water, <br> and the recent ion parameters by Kohagen et al. [4] for <br> CaCl_2.</p> <p>The Slipids force field parameters were downloaded from<br> http://mmkluster.fos.su.se/slipids/</p> <p>The ion parameters are available at<br> https://bitbucket.org/hseara/ions/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. These data<br> were collected once the adsorption and desorption of <br> CaCl_2 to the surface has reached equilibrium, namely<br> after 500 ns of simulation. Additionally, the initial <br> structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 4.6–> (.tpr) and the energy output file <br> (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p> <p>[4] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions<br> Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth<br> The Journal of Physical Chemistry B 2014 118 (28), 7902-7909<br> DOI: 10.1021/jp5005693</p>
POPC @ 310K, 130 mM of NaCl. Slipids with ions by Smith & Dang
<p>Simulations of a POPC bilayer with 130 mM of NaCl. <br> The goal was to study the effect of salt on the order <br> parameters of the lipid head group and the glycerol <br> backbone. The obtained results are reported in the <br> NMRlipids blog at http://nmrlipids.blogspot.fi</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 130 mM NaCl. The Slipids <br> model [1–3] is employed for lipids, tip3p model for water, <br> and the ion parameters by Smith and Dang [4] for NaCl. </p> <p>The Slipids force field parameters were downloaded from<br> http://mmkluster.fos.su.se/slipids/</p> <p>The ion parameters are available at<br> https://bitbucket.org/hseara/ions/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. Additionally,<br> the initial structure (.gro), topology (.top), index<br> file (.ndx), simulation paremeter file (.mdp), binary <br> run input file for GROMACS v. 4.6–> (.tpr) and the <br> energy output file (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p> <p>[4] Computer simulations of NaCl association in polarizable water<br> David E. Smith and Liem X. Dang <br> The Journal of Chemical Physics 1994 100, 3757-3766<br> DOI: 10.1063/1.466363</p>
POPC @ 310K, 450 mM of CaCl_2. Charmm36 with default Charmm ions
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. <br> The goal was to study the effect of salt on the order <br> parameters of the lipid head group and the glycerol <br> backbone for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The Charmm36 <br> model [1] is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the default Charmm<br> ion parameters (type CAL) for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained from http://mackerell.umaryland.edu/charmm_ff.shtml</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. These data<br> were collected after 1900 ns of simulation Additionally,</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.0–> (.tpr) and the energy output file <br> (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field <br> for Lipids: Validation on Six Lipid Types<br> Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, <br> Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, <br> Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor<br> The Journal of Physical Chemistry B 2010 114 (23), 7830-7843<br> DOI: 10.1021/jp101759q</p>
POPC @ 310K, 450 mM of CaCl_2. Slipids with default Amber ions
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. <br> The goal was to study the effect of salt on the order <br> parameters of the lipid head group and the glycerol <br> backbone for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The Slipids <br> model [1–3] is employed for lipids, tip3p model for water, <br> and the default amber ion parameters (type C0) for CaCl_2.</p> <p>The Slipids force field parameters were downloaded from<br> http://mmkluster.fos.su.se/slipids/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. These data<br> were collected after 1900 ns of simulation. Additionally,</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 4.6–> (.tpr) and the energy output file <br> (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p>
POPC with varying amounts of cholesterol, 450 mM of CaCl_2. Charmm36 with default Charmm ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Charmm36 model [1,2] is employed for lipids, the Charmm compatible variant of the tip3p model for water, and the default Charmm ion parameters (type CAL) for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained from http://mackerell.umaryland.edu/charmm_ff.shtml .<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 2 µs long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 5.0->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor, The Journal of Physical Chemistry B 2010 114 (23), 7830–7843, DOI: 10.1021/jp101759q</p> <p>[2] Update of the Cholesterol Force Field Parameters in CHARMM. Joseph B. Lim, Brent Rogaski, and Jeffery B. Klauda, The Journal of Physical Chemistry B 2012 116 (1), 203–210, DOI: 10.1021/jp207925m</p>
POPC with varying amounts of cholesterol, 450 mM of CaCl_2. Charmm36 with ECC-scaled ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Charmm36 model [1,2] is employed for lipids, the Charmm compatible variant of the tip3p model for water, and the recent ion parameters by Kohagen et al. [3] for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained Charmm-GUI [4], and the ion parameters are available at https://bitbucket.org/hseara/ions/ . IMPORTANT: The simulations are performed with version 1.7 obtained from Charmm-GUI, and this version is known to have an issue with the multiplicity of dihedrals in Gromacs output files, see http://www.charmm-gui.org/?doc=log . <br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 800 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 5.0->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor, The Journal of Physical Chemistry B 2010 114 (23), 7830–7843, DOI: 10.1021/jp101759q</p> <p>[2] Update of the Cholesterol Force Field Parameters in CHARMM. Joseph B. Lim, Brent Rogaski, and Jeffery B. Klauda, The Journal of Physical Chemistry B 2012 116 (1), 203–210, DOI: 10.1021/jp207925m</p> <p>[3] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions. Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth, The Journal of Physical Chemistry B 2014 118 (28), 7902-7909, DOI: 10.1021/jp5005693</p> <p>[4] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, <br> Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im, Journal of Chemical Theory and Computation 2016 12 (1), 405-413, DOI: 10.1021/acs.jctc.5b00935</p>
POPC with varying amounts of cholesterol, 130 mM of NaCl. Charmm36 with default Charmm ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 130 mM of NaCl performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Charmm36 model [1,2] is employed for lipids, the Charmm compatible variant of the tip3p model for water, and the standard Charmm ion parameters for NaCl [3].</p> <p>The Charmm36 force field parameters were obtained Charmm-GUI [4]. IMPORTANT: The simulations are performed with version 1.7 obtained from Charmm-GUI, and this version is known to have an issue with the multiplicity of dihedrals in Gromacs output files, see http://www.charmm-gui.org/?doc=log . <br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 200 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 5.0->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor, The Journal of Physical Chemistry B 2010 114 (23), 7830–7843, DOI: 10.1021/jp101759q</p> <p>[2] Update of the Cholesterol Force Field Parameters in CHARMM. Joseph B. Lim, Brent Rogaski, and Jeffery B. Klauda, The Journal of Physical Chemistry B 2012 116 (1), 203–210, DOI: 10.1021/jp207925m</p> <p>[3] Control of Ion Selectivity in LeuT: Two Na+ Binding Sites with Two Different Mechanisms. Sergei Y. Noskov and Benoit Roux, Journal of Molecular Biology 2008 377 (3), 804–818, DOI:10.1016/j.jmb.2008.01.015</p> <p>[4] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, <br> Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im, Journal of Chemical Theory and Computation 2016 12 (1), 405-413, DOI: 10.1021/acs.jctc.5b00935</p>
POPC with varying amounts of cholesterol, 450 mM of CaCl_2. Slipids with ECC-scaled ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. Additionally, simulations with 0% cholesterol are repeated at 330 K, 350 K, and 370 K. The Slipids model [1–3] is employed for lipids, tip3p model for water, and the recent ion parameters by Kohagen et al. [4] for CaCl_2. The Slipids force field parameters are available at http://www.fos.su.se/~sasha/SLipids/ and the ion parameters are available at https://bitbucket.org/hseara/ions/<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 600 ns long (800 ns long for systems at elevated temperatures) with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 4.6->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p> <p>[4] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions. Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth, The Journal of Physical Chemistry B 2014 118 (28), 7902-7909, DOI: 10.1021/jp5005693</p>
POPC with varying amounts of cholesterol, 450 mM of CaCl_2. Slipids with default Amber ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Slipids model [1–3] is employed for lipids, tip3p model for water, and the default amber ion parameters (type C0) for CaCl_2. The Slipids force field parameters are available at http://www.fos.su.se/~sasha/SLipids/ .<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 2 µs long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 4.6->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e<br> [2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n<br> [3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p> <p> </p>
POPC with varying amounts of cholesterol, 130 mM of NaCl. Slipids with ECC-scaled ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 130 mM of NaCl performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Slipids model [1–3] is employed for lipids, tip3p model for water, and the and the recent ion parameters by Kohagen et al. [4] for NaCl. The Slipids force field parameters are available at http://www.fos.su.se/~sasha/SLipids/ and the ion parameters are available at https://bitbucket.org/hseara/ions/<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 200 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 4.6->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p> <p>[4] Accounting for Electronic Polarization Effects in Aqueous Sodium Chloride via Molecular Dynamics Aided by Neutron Scattering. Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth, The Journal of Physical Chemistry B 2016 120 (8), 1454–1460, DOI: 10.1021/acs.jpcb.5b05221</p> <p> </p>
POPC with varying amounts of cholesterol, 130 mM of NaCl. Slipids with ions by Smith & Dang
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 130 mM of NaCl performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. Additionally, simulations with 0% cholesterol are repeated at 330 K, 350 K, and 370 K. The Slipids model [1–3] is employed for lipids, tip3p model for water, and the ion parameters by Smith and Dang [4] for NaCl. The Slipids force field parameters are available at http://www.fos.su.se/~sasha/SLipids/ and the ion parameters are available at https://bitbucket.org/hseara/ions/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 200 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 4.6->) (.tpr) are provided for each system. The common simulation parameter file can be downloaded from another entry at https://doi.org/10.5281/zenodo.259341.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p> <p>[4] Computer simulations of NaCl association in polarizable water. David E. Smith and Liem X. Dang, The Journal of Chemical Physics 1994 100, 3757-3766, DOI: 10.1063/1.466363</p>
and metatarsal trichobothria as well as the bristles and the tibial and metatarsal bristleshaped hairs are drawn but no normal hairs; 6) retrolateral aspect of the left retroclaw IV; 7) genital area in front of the epigastral furrow in which no epiandrous gland spigots are recognizable. Not all of the hairs anteriorly of the pit are drawn; 8) outline of the anterior spinnerets, ventral aspect; 9) retrolateral aspect of the right pedipalpus; 10) prolateral aspect of the right pedipalpus. Only two of the long retrolateral bristle-shaped cymbial hairs are drawn; 11) ventral aspect of the right pedipalpus; 12) slightly different retroventral aspects of the distal part of the right pedipalpus. C = conductor, E = embolus, M = median apophysis, O = proventral-distal outgrowth of the pedipalpal tibia. Scale bars 0.5 mm in figs. 1-2 and 5, 0.05 in fig. 4 and 6, 0.1 in fig. 7, 0.2 in the remaining figs; in On European Spiders Of The Nominal Families Liocranidae, Miturgidae And Zoridae (Araneae), With Descriptions Of New Taxa
and metatarsal trichobothria as well as the bristles and the tibial and metatarsal bristleshaped hairs are drawn but no normal hairs; 6) retrolateral aspect of the left retroclaw IV; 7) genital area in front of the epigastral furrow in which no epiandrous gland spigots are recognizable. Not all of the hairs anteriorly of the pit are drawn; 8) outline of the anterior spinnerets, ventral aspect; 9) retrolateral aspect of the right pedipalpus; 10) prolateral aspect of the right pedipalpus. Only two of the long retrolateral bristle-shaped cymbial hairs are drawn; 11) ventral aspect of the right pedipalpus; 12) slightly different retroventral aspects of the distal part of the right pedipalpus. C = conductor, E = embolus, M = median apophysis, O = proventral-distal outgrowth of the pedipalpal tibia. Scale bars 0.5 mm in figs. 1-2 and 5, 0.05 in fig. 4 and 6, 0.1 in fig. 7, 0.2 in the remaining figs;
Scandy-pro-2021-08-30-t20-29-19-867-z-mm
Scan of a small statue Source: Objaverse 1.0 / Sketchfab
Figure S1-S3: The ARPE-19 cells were cultured in low glucose (5 mM), osmotic Control and high glucose (25 mM) medium.
<p><span>Figure S1-S3: The ARPE-19 cells were cultured in low glucose (5 mM), osmotic Control and high glucose (25 mM) medium.</span></p>
Supplementary material 4 from: Vanegas-Ríos JA, Serra Alanís WS, Azpelicueta MM, Litz T, Malabarba LR (2024) Population variation of Diapoma pampeana (Characiformes, Characidae, Stevardiinae) from an isolated coastal drainage in Uruguay, with new records: comparing morphological and molecular data. Zoosystematics and Evolution 100(1): 69-85. https://doi.org/10.3897/zse.100.112778
Cluster analysis (Ward's method) of size-corrected morphometric data of analyzed specimens of Diapoma pampeana
Heart Disease Dataset - Carotid Intima-Media Thickness Test (CIMT) in mm
<p>This dataset contains heart disease related patient information along with complications according to CIMT thickness in mm.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.